I would also counsel that you take the rest day. As someone who completed the whole programme (having done it absolutely properly!) I struggled with shin pain from weeks 5 onwards, and took extra rest time - but still ended up having to have treatment from my osteopath to sort me out.
I'm allowed to run now, but I have to take two rest days rather than one to make sure that I don't suffer again.
And stretching afterwards is hugely important - it's this which helps to keep your muscles supple and to prevent soreness.
Re apps, I use Get Running, which tells you when to start/stop, and when you've reached the halfway point if you need to turn round. Map My Run also has an app which you can use too - I use both. Get Running just tells you how many minutes to run form whereas Map My Run records how far you have run, and also gives you info about your pace and how many calories you will have burnt.
It's complicated though
. I start my music playing, then launch Get Running, and then when I get to the running part (after the 5 minute brisk walk to warm up) start Map My Run.